Brittany Renshaw and Dr. David Allred, Physics and Astronomy
My research has focused on a genus of endolithic cyanobacteria called Chroococcidiopsis. These organisms are found in rocks from Antarctica to thermal springs and other arid or highly saline environments (Friedmann and Friedmann 1995). The organisms inhabit limestone and sandstone, appearing as a green band near the surface. The long-term goal for the project is the use of Chroococcidiopsis, because of its ability to survive in extreme habitats, as a model organism for designing tests to determine if there is life on Mars. With NASA’s renewed interest in a trip to Mars, a study of this organism would be a useful archetype for a study of the possibility of life on Mars.
The first step in the project was the collection of samples of Dakota sandstone containing Chroococcidiopsis from southern Utah near the Mars Desert Research Station. Next, I separated the organism from the sandstone in which it is embedded. Chroococcidiopsis is a very slow growing organism; therefore, culturing would have been impractical, instead I extracted the DNA directly from the samples. I used a soil extraction kit to isolate the DNA from Chroococcidiopsis. DNA was isolated from several of the samples and then tested on a gel that confirmed the presence of DNA but was not able to show purity. The next step was amplification of the DNA using polymerase chain reaction (PCR). To run the PCR, I used published primers for the 16S segment of the genome—a highly conserved sequence of DNA. Despite repeated attempts, I was unable to obtain a successful PCR. To continue testing the PCR, more DNA will need to be isolated. The PCR setback has become a bottleneck to the project.
Through further investigation, I have determined three possible conditions that could account for the failure of the DNA to amplify: the wrong PCR conditions, poor/old samples, or the wrong primers. If the PCR conditions are wrong, the solution is to contact other researchers who have worked with this organism to determine optimal conditions or to use a PCR optimization kit to test various parameters in the PCR. If the samples were old or poorly isolated, it would simply be a matter of resampling and isolating the DNA again. The last possibility would be the most challenging—the wrong primers. I could contact other researchers for the primers they have used, but if that failed, I would most likely have to have primers designed from published 16S sequences. Each of these routes is being investigated with the hope of finding a working PCR.
Once the DNA is amplified, I will be able to continue with my project. I will submit the DNA for sequencing and then do an analysis using several programs outlined in my proposal. I am currently working on forming collaboration with other researchers investigating Chroococcidiopsis to help consolidate resources and share information.
In April 2005, I presented my then current progress on my research project at the Utah Academy of Science, Arts, and Letters Annual Conference. I gave two ten-minute PowerPoint presentation—one at the Conference and one at BYU to the Mars Research Group.
In conclusion, I have been able to successfully sample and isolate DNA from Chroococcidiopsis. With further experimentation, I expect to produce a working PCR. Once the PCR works, I will be able to sequence the DNA and conduct my genetic analysis. The analysis will help to classify the organism and determine its phylogenetic relationship to other organisms. This project has been a great opportunity for me as I have experienced both the successes and the setbacks that occur in research. I have greatly enjoyed the victories, but from the failures I have learned much more—how to get back up and keep working.